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antgonzaantgonza
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2 parents 3842dc6 + f72766c commit 68ecebc

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lines changed

‎src/qp_klp/Workflows.py‎

Lines changed: 6 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -503,9 +503,9 @@ def _compare_samples_against_qiita(self):
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results_sn = self._process_sample_names(p_name, qiita_id,
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samples)
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msgs.append("Number of values in sheet that aren't sample-names in"
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" Qiita: %s" % len(results_sn[0]))
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rsn = results_sn[0]
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msgs.append('Number of sample-names not in Qiita: '
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f'{len(rsn)}; {list(rsn)[:3]}')
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use_tids = False
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@@ -517,8 +517,9 @@ def _compare_samples_against_qiita(self):
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# check for possible match w/tube-ids, if defined in project.
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results_tid = self._process_tube_ids(qiita_id, samples)
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if results_tid:
520-
msgs.append("Number of values in sheet that aren't "
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"tube-ids in Qiita: %s" % len(results_tid[0]))
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rtid = results_tid[0]
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msgs.append('Number of tube-ids not in Qiita: '
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f'{len(rtid)}; {list(rtid)[:3]}')
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if len(results_tid[0]) == 0:
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# all values were matched to tube-ids.

‎src/sequence_processing_pipeline/Pipeline.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -799,7 +799,7 @@ def _parse_project_name(self, project_name, short_names):
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"""
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Split fully-qualified project_name into a project_name and a qiita-id
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if possible. Else return project_name and None.
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:param project_name: A fully-qualified project name e.g: Feist_1161.
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:param project_name: A fully-qualified project name e.g: StudyB_1161.
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:param short_names: True returns orig. value. False returns name only.
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:return: Tuple (project-name, qiita-id)
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"""

‎tests/data/20230101_XX99999999_99_LOL99999-9999.NYU_BMS_Melanoma_13059.1.tsv‎

Lines changed: 10 additions & 10 deletions
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
experiment_design_description well_description library_construction_protocol platform run_center run_date run_prefix sequencing_meth center_name center_project_name instrument_model runid lane sample_project sample_well sample_name index i7_index_id sample_plate index2 i5_index_id raw_reads_r1r2 quality_filtered_reads_r1r2 non_host_reads fraction_passing_quality_filter fraction_non_human old_sample_name
2-
test description 13059.SP331130A04 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 G17 SP331130A04 GGAAGGAT iTru7_110_08 SAMPLE CACAAGTC iTru5_01_E SP331130A-4
3-
test description 13059.AP481403B02 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 O8 AP481403B02 TCCGTATG iTru7_111_08 SAMPLE ACAGCTCA iTru5_03_B AP481403B-2
4-
test description 13059.LP127829A02 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 D24 LP127829A02 CCGGAATT iTru7_112_06 SAMPLE TTCGTACC iTru5_05_A LP127829A-2
5-
test description 13059.BLANK3.3B Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 H18 BLANK3.3B GGAAGGAT iTru7_110_08 SAMPLE CTACAGTG iTru5_02_C BLANK3.3B
6-
test description 13059.EP529635B02 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 B19 EP529635B02 CGATAGAG iTru7_111_01 SAMPLE AGCGTGTT iTru5_02_F EP529635B-2
7-
test description 13059.EP542578B04 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 O22 EP542578B04 AGTCTCAC iTru7_112_04 SAMPLE GTTCATGG iTru5_04_C EP542578B-4
8-
test description 13059.EP446602B01 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 L3 EP446602B01 AACCGTTC iTru7_110_02 SAMPLE TTGCCACT iTru5_01_B EP446602B-1
9-
test description 13059.EP121011B01 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 B24 EP121011B01 AGTTGGCT iTru7_112_05 SAMPLE TGGCACTA iTru5_04_H EP121011B-1
10-
test description 13059.EP636802A01 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 I2 EP636802A01 AAGTCGAG iTru7_109_05 SAMPLE TGGCATGT iTru5_05_G EP636802A-1
11-
test description 13059.SP573843A04 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 NYU_BMS_Melanoma_13059 F9 SP573843A04 CTTCGTTC iTru7_111_11 SAMPLE CGTTATGC iTru5_03_G SP573843A-4
2+
test description 13059.SP331130A04 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 G17 SP331130A04 GGAAGGAT iTru7_110_08 SAMPLE CACAAGTC iTru5_01_E SP331130A-4
3+
test description 13059.AP481403B02 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 O8 AP481403B02 TCCGTATG iTru7_111_08 SAMPLE ACAGCTCA iTru5_03_B AP481403B-2
4+
test description 13059.LP127829A02 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 D24 LP127829A02 CCGGAATT iTru7_112_06 SAMPLE TTCGTACC iTru5_05_A LP127829A-2
5+
test description 13059.BLANK3.3B Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 H18 BLANK3.3B GGAAGGAT iTru7_110_08 SAMPLE CTACAGTG iTru5_02_C BLANK3.3B
6+
test description 13059.EP529635B02 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 B19 EP529635B02 CGATAGAG iTru7_111_01 SAMPLE AGCGTGTT iTru5_02_F EP529635B-2
7+
test description 13059.EP542578B04 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 O22 EP542578B04 AGTCTCAC iTru7_112_04 SAMPLE GTTCATGG iTru5_04_C EP542578B.4
8+
test description 13059.EP446602B01 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 L3 EP446602B01 AACCGTTC iTru7_110_02 SAMPLE TTGCCACT iTru5_01_B EP446602B.1
9+
test description 13059.EP121011B01 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 B24 EP121011B01 AGTTGGCT iTru7_112_05 SAMPLE TGGCACTA iTru5_04_H EP121011B.1
10+
test description 13059.EP636802A01 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 I2 EP636802A01 AAGTCGAG iTru7_109_05 SAMPLE TGGCATGT iTru5_05_G EP636802A.1
11+
test description 13059.SP573843A04 Knight Lab Kapa HyperPlus Illumina IGM 2017-09-02 SAMPLE sequencing by synthesis UCSD SAMPLE Illumina HiSeq 4000 211021_A00000_0000_SAMPLE 1 StudyA_13059 F9 SP573843A04 CTTCGTTC iTru7_111_11 SAMPLE CGTTATGC iTru5_03_G SP573843A.4

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