removed Bio Alphabet from dependencies. 'tracer test' fails because o…

Dockerfile

@@ -8,6 +8,7 @@ FROM debian:latest
 RUN apt-get update && apt-get -y upgrade
 RUN apt-get -y install wget curl unzip build-essential zlib1g-dev git python3 python3-pip bowtie2 default-jre procps cmake libcairo2-dev pkg-config samtools jellyfish salmon
 
+
 #Trinity - depends on zlib1g-dev and openjdk-8-jre installed previously
 RUN wget https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v2.11.0/trinityrnaseq-v2.11.0.FULL.tar.gz
 RUN tar xvzf trinityrnaseq-v2.11.0.FULL.tar.gz  && rm trinityrnaseq-v2.11.0.FULL.tar.gz
@@ -17,10 +18,12 @@ RUN cd /trinityrnaseq-v2.11.0  && make
 #and then on top of that, the environmental variable thing facilitates the creation of a shell wrapper. fun
 RUN wget ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/1.7.0/ncbi-igblast-1.7.0-x64-linux.tar.gz
 RUN tar -xzvf ncbi-igblast-1.7.0-x64-linux.tar.gz && rm ncbi-igblast-1.7.0-x64-linux.tar.gz
-RUN cd /ncbi-igblast-1.7.0/bin/ && wget -r ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data && \
-	wget -r ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file && \
-	mv ftp.ncbi.nih.gov/blast/executables/igblast/release/internal_data . && \
-	mv ftp.ncbi.nih.gov/blast/executables/igblast/release/optional_file . && \
+RUN cd /ncbi-igblast-1.7.0/bin/ && wget -r ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/old_internal_data && \
+	wget -r ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/old_optional_file && \
+	mv ftp.ncbi.nih.gov/blast/executables/igblast/release/old_internal_data . && \
+	mv ftp.ncbi.nih.gov/blast/executables/igblast/release/old_optional_file . && \
+	ln -s old_internal_data internal_data && \
+	ln -s old_optional_file optional_file && \
 	rm -r ftp.ncbi.nih.gov
 
 #aligners - kallisto and salmon
@@ -34,16 +37,30 @@ RUN apt-get -y install graphviz
 
 #tracer proper
 COPY . /tracer
+
+
+#placing a preconfigured tracer.conf in ~/.tracerrc
+RUN cp /tracer/docker_helper_files/docker_tracer.conf ~/.tracerrc
+
+
+## update some python packages to remove install version error
+RUN pip3 install numpy --upgrade
+RUN pip3 install pyparsing --upgrade
 RUN cd /tracer && pip3 install -r docker_helper_files/requirements_stable.txt && python3 setup.py install
 
+
+################################################################
 #obtaining the transcript sequences. no salmon/kallisto indices as they make dockerhub unhappy for some reason
+
+
 RUN mkdir GRCh38 && cd GRCh38 && wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_27/gencode.v27.transcripts.fa.gz && \
 	gunzip gencode.v27.transcripts.fa.gz && python3 /tracer/docker_helper_files/gencode_parse.py gencode.v27.transcripts.fa && rm gencode.v27.transcripts.fa
+
+
 RUN mkdir GRCm38 && cd GRCm38 && wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M15/gencode.vM15.transcripts.fa.gz && \
 	gunzip gencode.vM15.transcripts.fa.gz && python3 /tracer/docker_helper_files/gencode_parse.py gencode.vM15.transcripts.fa && rm gencode.vM15.transcripts.fa
 
-#placing a preconfigured tracer.conf in ~/.tracerrc
-RUN cp /tracer/docker_helper_files/docker_tracer.conf ~/.tracerrc
 
 #this is a tracer container, so let's point it at a tracer wrapper that sets the silly IgBLAST environment variable thing
 ENTRYPOINT ["bash", "/tracer/docker_helper_files/docker_wrapper.sh"]
+

tracer

@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 ############################################################################## 
 # TraCeR - a tool to reconstruct TCR sequences from single-cell RNA-seq data #

tracerlib/core.py

@@ -2,7 +2,10 @@
 from collections import Counter, defaultdict
 
 import six
-from Bio.Alphabet import generic_dna
+try:
+  from Bio.Alphabet import generic_dna
+except:
+      print("Bio.Alphabet IUPAC not imported.  Possibly missing, possibly you are runing a modern version of python that doesn't need it")
 from Bio.Seq import Seq
 import pdb
 

tracerlib/tracer_func.py

@@ -26,7 +26,12 @@
 import networkx as nx
 import six
 from Bio import SeqIO
-from Bio.Alphabet import IUPAC
+
+try:
+  from Bio.Alphabet import IUPAC
+except:
+  print("Bio.Alphabet IUPAC not imported.  Possibly missing, possibly you are runing a modern version of python that doesn't need it")
+
 from Bio.Seq import Seq
 
 from tracerlib.core import Cell, Recombinant, Invar_cell
@@ -462,8 +467,10 @@ def is_rearrangement_productive(seq):
         in_frame = True
     else:
         in_frame = False
-
-    seq = Seq(seq, IUPAC.unambiguous_dna)
+    # original    
+    #seq = Seq(seq, IUPAC.unambiguous_dna)
+    # modified
+    seq = Seq(seq)
     aa_seq = seq.translate()
     contains_stop = "*" in aa_seq
 
@@ -553,7 +560,8 @@ def get_fasta_line_for_contig_assembly(trinity_seq, hit_table, locus, IMGT_seqs,
     end_base_removal_count = (1 - end_padding) % 3
 
     seq = trinity_seq[start_base_removal_count:-(end_base_removal_count)]
-    seq = Seq(seq, IUPAC.unambiguous_dna)
+    # seq = Seq(seq, IUPAC.unambiguous_dna)
+    seq = Seq(seq)
     aa_seq = seq.translate()
     contains_stop = "*" in aa_seq