Add RiboCode intermediate test files

README.md

@@ -436,6 +436,10 @@ The earth sciences folder contain subfolders for different data formats encounte
       - plastid
         - Homo_sapiens.GRCh38.111_chr20_rois.txt: metagene generated from Homo_sapiens.GRCh38.111_chr20.gtf using plastid `metagene generate` command
         - SRX11780887_p_offsets.txt: p-site offsets genereated from SRX11780887_chr20.bam and Homo_sapiens.GRCh38.111_chr20.gtf using plastid `psite` command
+      - ribocode
+        - genome_updated.gtf.gz: GTF with gene names updated via ribocode/gtfupdate, compressed for efficient storage
+        - annotation.tar.gz: Tarball containing annotation directory output from ribocode/prepare for testing ribocode/metaplots and ribocode/ribocode modules
+        - test_pre_config.txt: P-site configuration file output from ribocode/metaplots for testing ribocode/ribocode module
       - salmon.merged.gene_counts_length_scaled.tsv: Example matrix containing both Riboseq and RNA-seq runs, suitable for translational efficiency analysis
       - samplesheet.csv: Sample sheet corresponding to salmon.merged.gene_counts_length_scaled.tsv
   - illumina

data/genomics/homo_sapiens/riboseq_expression/ribocode/README.md

@@ -0,0 +1,21 @@
+# RiboCode module test files
+
+Intermediate outputs for testing ribocode modules.
+
+## genome_updated.gtf.gz
+
+Compressed output from `ribocode/gtfupdate` module. Use with GUNZIP to decompress.
+
+## annotation.tar.gz
+
+Tarball of output from `ribocode/prepare` module containing:
+
+- `transcripts.pickle` - Pickled transcript annotation data
+- `transcripts_cds.txt` - CDS information for transcripts
+- `transcripts_sequence.fa` - Transcript sequences in FASTA format
+
+Use with UNTAR module to extract before passing to ribocode modules.
+
+## test_pre_config.txt
+
+P-site offset configuration file generated by `ribocode/metaplots` module.

data/genomics/homo_sapiens/riboseq_expression/ribocode/test_pre_config.txt

@@ -0,0 +1,14 @@
+
+#SRX11780887.Aligned.toTranscriptome.out.bam
+#read_length	proportion(per total mapped reads)	predicted_psite	f0_sum	f1_sum	f2_sum	f0_percent	pvalue1	pvalue2	pvalue_combined
+# 24	8.99%	11	67	15	12	71.28%	0.07871445393610088	0.05335433821437063	0.016162538604212823
+# 28	15.31%	12	91	20	15	72.22%	0.07861401169693945	0.09699270034475277	0.027516362010860176
+# 29	7.88%	5	24	12	4	60.00%	0.1753983517655281	0.012925525021785452	0.012691976002796142
+# 31	2.24%	4	13	10	2	52.00%	0.21618695127160653	0.0319825310473083	0.031088180227879778
+# 25	12.49%	12	39	20	14	53.42%	0.10425804304619735	0.0065634957174151385	0.004107077153617081
+# 27	16.68%	11	111	18	25	72.08%	0.23199775215455887	0.39876920839246044	0.24221361451859125
+# 30	4.25%	19	22	13	12	46.81%	0.5	0.6184876997235025	0.5844147952291188
+# 26	13.47%	7	72	9	12	77.42%	0.010332180556073796	0.01245294156089251	0.000635986019988928
+
+# SampleName	AlignmentFile	Stranded(yes/reverse)	P-siteReadLength	P-siteLocations
+SRX11780887.Aligned.toTranscriptome.out	SRX11780887.Aligned.toTranscriptome.out.bam	yes	24,25,26,27,28,29,30,31	11,12,7,11,12,5,19,4